Mitigating pather interest while freeport is on wouldn't make it all that useful. Freeport is desirable in early-midgame to grow colonies faster, and in late-game for more accessibility (in late game, you've also got enough AI cores that reducing interest won't do much). Also, Pather cell success rates depend on stability, so, as it is, turning off freeport will essentially end them.
Given that nothing really threatens colonies on the ground (the player will always do whatever's necessary to prevent such an attack), I think making the shield significant would entail it providing some other kind of benefit. The shield is a visual reference to Star Control II, so maybe drawing on that for inspiration would help. Shielded planets had only one interaction with the outside world - an orbiting station that provided logistical assistance to passing fleets. The world below was tightly regulated (for its own good), and had very little conflict, accordingly.
We probably don't want to do anything too drastic, but having the shield consume a large amount of some material (volatiles, transplutonics, equipment?), add some stability (living under a giant shield tends to dissuade lawbreakers - it's an ever-present reminder that you're living under someone's authority), and provide a relatively small access penalty. Essentially, it'd be something that allows freeport and commerce to be reliably used together on planets where you don't have enough stability to otherwise do so. Planets pay a flat premium, plus a little bit of access, and have to have a large industrial base behind them, but, in exchange, stability is no longer a problem as long as every other mitigating action is also taken.
As for making it an industry, I'm not sure how to make that worthwhile. Mentioned before that M+R+HI+C is pretty unbeatable, as is M+F+LI+C. Luddic Majority + F+LI+C is sort of competitive, but means you're stuck importing organics unless you have another source. One route might be to treat it as a faction-wide vanity project - high cost, including maintenance, high resource consumption, and maybe you can only build one, but putting it on your largest colony adds stability and fleet-size everywhere (partially due to sheer impressiveness, and partially because a stable, well-defended center of government makes everything move more smoothly).